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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Sep 24, 2024
1 parent 32923f9 commit 0522a03
Showing 1 changed file with 62 additions and 65 deletions.
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
import logging
from dataclasses import dataclass

import numpy as np
from bravado.client import SwaggerClient
from dataclasses import dataclass

from missense_kinase_toolkit.databases.api_schema import SwaggerAPIClient

Expand All @@ -12,119 +12,119 @@
# start/end and colors courtesy of OpenCADD
DICT_POCKET_KLIFS_REGIONS = {
"I": {
"start": 1,
"start": 1,
"end": 3,
"contiguous": True,
"color": "khaki",
},
},
"g.l": {
"start": 4,
"start": 4,
"end": 9,
"contiguous": True,
"color": "green",
},
},
"II": {
"start": 10,
"start": 10,
"end": 13,
"contiguous": True,
"color": "khaki",
},
},
"III": {
"start": 14,
"start": 14,
"end": 19,
"contiguous": False,
"color": "khaki",
},
},
"αC": {
"start": 20,
"start": 20,
"end": 30,
"contiguous": True,
"color": "red",
},
},
"b.l": {
"start": 31,
"start": 31,
"end": 37,
"contiguous": True,
"color": "green",
},
},
"IV": {
"start": 38,
"start": 38,
"end": 41,
"contiguous": False,
"color": "khaki",
},
},
"V": {
"start": 42,
"start": 42,
"end": 44,
"contiguous": True,
"color": "khaki",
},
},
"GK": {
"start": 45,
"start": 45,
"end": 45,
"contiguous": True,
"color": "orange",
},
},
"hinge": {
"start": 46,
"end": 48,
"start": 46,
"end": 48,
"contiguous": True,
"color": "magenta",
},
},
"linker": {
"start": 49,
"start": 49,
"end": 52,
"contiguous": True,
"color": "cyan",
},
},
"αD": {
"start": 53,
"end": 59,
"start": 53,
"end": 59,
"contiguous": False,
"color": "red",
},
},
"αE": {
"start": 60,
"start": 60,
"end": 64,
"contiguous": True,
"color": "red",
},
},
"VI": {
"start": 65,
"start": 65,
"end": 67,
"contiguous": True,
"color": "khaki",
},
},
"c.l": {
"start": 68,
"start": 68,
"end": 75,
"contiguous": True,
"color": "darkorange",
},
"VII": {
"start": 76,
"end": 78,
"start": 76,
"end": 78,
"contiguous": False,
"color": "khaki",
},
},
"VIII": {
"start": 79,
"start": 79,
"end": 79,
"contiguous": True,
"color": "khaki",
},
},
"xDFG": {
"start": 80,
"start": 80,
"end": 83,
"contiguous": True,
"color": "cornflowerblue",
},
},
"a.l": {
"start": 84,
"start": 84,
"end": 85,
"contiguous": False,
"color": "cornflowerblue",
},
},
}
"""dict[str, dict[str, int | bool | str]]: Mapping KLIFS pocket region to start and end indices, \
boolean denoting if subsequent regions are contiguous, and colors."""
Expand Down Expand Up @@ -205,8 +205,7 @@ def align_klifs_pocket_to_uniprot_seq(
list_idx = None
else:
list_idx = return_idx_of_substring_in_superstring(
str_uniprot,
substring_klifs_narm
str_uniprot, substring_klifs_narm
)
return substring_klifs, list_idx

Expand Down Expand Up @@ -256,14 +255,14 @@ def iterate_klifs_alignment(
)

str_klifs, list_substring_idx = align_klifs_pocket_to_uniprot_seq(
idx_start = klifs_idx_start,
idx_end = klifs_idx_end,
str_uniprot = string_uniprot,
str_klifs = string_klifs,
idx_start=klifs_idx_start,
idx_end=klifs_idx_end,
str_uniprot=string_uniprot,
str_klifs=string_klifs,
)
list_klifs_substr_actual.append(str_klifs)

# if None KLIFS all "-"; if multiple KLIFS regions,
# if None KLIFS all "-"; if multiple KLIFS regions,
# concatenate with contiguous regions to identify single match
if list_substring_idx is not None and len(list_substring_idx) > 1:
bool_cont = dict_klifs[klifs_region_start]["contiguous"]
Expand All @@ -280,23 +279,25 @@ def iterate_klifs_alignment(
dict_klifs[klifs_region_end]["end"],
)
str_klifs, list_substring_idx = align_klifs_pocket_to_uniprot_seq(
idx_start = klifs_idx_start,
idx_end = klifs_idx_end,
str_uniprot = string_uniprot,
str_klifs = string_klifs,
idx_start=klifs_idx_start,
idx_end=klifs_idx_end,
str_uniprot=string_uniprot,
str_klifs=string_klifs,
)
# if concat with previous, offset by length of preceding KLIFS region with gaps removed
if not bool_cont and \
list_substring_idx is not None and \
len(list_substring_idx) != 0:
if (
not bool_cont
and list_substring_idx is not None
and len(list_substring_idx) != 0
):
len_offset = len(remove_gaps_from_klifs(str_klifs)) - len_klifs
list_substring_idx = [i + len_offset for i in list_substring_idx]

list_klifs_region.append(klifs_region_start + ":" + klifs_region_end)
list_klifs_substr_match.append(str_klifs)
list_substring_idxs.append(list_substring_idx)

#TODO: if no match, try to find match with gaps
# TODO: if no match, try to find match with gaps
# list_idx_no_match = [idx for idx, i in enumerate(list_substring_idxs)\
# if not i and i is None]
# for idx in list_idx_no_match:
Expand All @@ -306,7 +307,7 @@ def iterate_klifs_alignment(
# except:
# idx_start = 0
# idx_end = list_substring_idxs[idx+1] + len(remove_gaps_from_klifs(list_klifs_substr_actual[idx+1]))
# substr_uniprot =
# substr_uniprot =
# substr_klifs = list_klifs_substr_actual[idx]

dict_out = {
Expand Down Expand Up @@ -503,9 +504,7 @@ def __post_init__(self):
pass

@staticmethod
def remove_gaps_from_klifs(
klifs_string: str
) -> str:
def remove_gaps_from_klifs(klifs_string: str) -> str:
"""Remove gaps from KLIFS pocket sequence.
Parameters
Expand All @@ -518,14 +517,13 @@ def remove_gaps_from_klifs(
klifs_pocket_narm : str
KLIFS pocket sequence without gaps (i.e., "-" removed)
"""
"""
klifs_pocket_narm = "".join([i for i in klifs_string if i != "-"])
return klifs_pocket_narm

@staticmethod
def return_idx_of_substring_in_superstring(
superstring: str,
substring: str
superstring: str, substring: str
) -> list[int] | None:
"""
Expand Down Expand Up @@ -575,7 +573,6 @@ def align_klifs_pocket_to_uniprot_seq(
list_idx = None
else:
list_idx = self.return_idx_of_substring_in_superstring(
self.uniprotSeq,
substring_klifs_narm
self.uniprotSeq, substring_klifs_narm
)
return substring_klifs, list_idx

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